Signal processing techniques applied to coded representations of partially denatured DNA molecules will be used to construct complete denaturation maps of certain large DNA molecules including E. coli and yeast chromosomes. The procedure treats each molecule as a binary waveform (0 where the molecule is native, 1 where the molecule is denatured). The algorithm then aligns the set of DNA maps by a cross-correlation approach. Operating considerably faster than humans, the technique can analyze a set of 63 molecules in about 1 1/2 hours, producing an objective output with significantly better resolution of the denatured regions than was previously available. In addition the technique gives us the capacity to match and identify various species of molecules. We will begin using episomal DNA from E. coli; after completion of initial experiments we will attempt the mapping of a large DNA molecule such as that in a yeast chromosome.